End-game missions are missions you can do after you complete the main storyline on story mode by doing either the Liberation Army/Qubba Government or Workforce Merchant/Federation storyline. Noted that the sequence of each missions are random in every playthrough.
Qubba Government end-game missions
To start the end-game missions you first have to talk to Richard Weaver. You have to pick the dialogue options that refuse being a politician. (You still have the option to become a politician by revisit Rechard Weaver and ask about it even if your on mission)
Rescue Mission
In this mission you have to rescue a stranded caravan en route to Dagmar from Gamal Met. You have to find it and rescue the survivors as fast as you can to the nearest town. The easiest way is to start at Gamal Met and go to Dagmar. Richard Weaver will give you some money after you complete it.
Medical Emergency
In this mission Richard Weaver tells you that their is a medical emergency in Shadheen 71. He gives you a temporary companion that is a skilled doctor that you have to take to Shadheen 71. Richard Weaver will give you some money after you complete it.
Medical Emergency (2)
In this mission Richard Weaver tells you that there is an epidemic in Heiselle and you need to deliver medicine there. He gives you 2699g of medicine which you must deliver.
Rescue Mission
In this mission Richard Weaver tells you that a important public figure was kidnapped in the area around Toho Sands. You have to bring him to the nearest town. Richard Weaver will give you some money after you complete it.
Prisoner Escort
In this mission Richard Weaver tells you that a criminal is located in Arton and has to be transferred to Qubba, and that his old "friends" might try to attack you to get him out. You have to go to Arton and the prisoner will join you, then you go to Qubba and a notification will pop up telling you that the prisoner has been remanded into custody. Richard Weaver will give you 47,690 cash for it.
Prisoner Escort (2)
In this mission Richard Weaver tells you that a criminal is located in Sandstorm Basin and has to be transferred to Qubba.
Eliminate Bandits
In this mission Richard Weaver tells you that a gang of bandits operates close to Tara'koona and you must either capture or kill them.
Relocating citizens
In this mission Richard Weaver tells you that some citizens need to be moved from one city to another (usually in the Federation area). They will automatically join your caravan when you visit the first city.
Delivering goods
In this mission Richard Weaver tells you that Gamal Met requires some cemet and gives you 99g of cemet to deliver to Gamal Met.
Workforce Merchants end-game missions
To start the end-game missions you first have to talk to Huli Kitsune. You receive some money when the mission is completed. These missions become available during the storyline after you receive the metal plaque that marks your position as the best worker of the Workforce Merchants.
The missions will not appear on your missions log at that time nor after the storyline is completed. So, take notes if you have a poor memory. Huli Kitsune will remind you what you need to do if you ask her while the mission is in progress.
Help the Janubi Police
Defeat 10 groups (in total) of Janubi bandits, Scavengers, and/or Shinobi Pillagers. Reward: 20,000.
Deliver a Package
Deliver a package (weight 0.02 kg.) from Tifk to a named person in another town. The person may be Calvin, Captain Mustaparta, Solanum III, or the Chief Guard. Reward: depends on how quickly you complete the mission.
Escort convoy
Escort and protect a caravan of slaves from Tifk to another town.
Transport Slaves
Transport 17 slaves from Calvin in New Serino to Tifk. Calvin will give you some supplies for the trip to Tifk. The first time you receive this mission you get the Gulde to Slaving pamphlet. This mission does not change your Slaver reputation. Reward: 35,000.